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Charrier M, Leroux I, Pichon J, Schleder C, Larcher T, Hamel A, Magot A, Péréon Y, Lamirault G, Tremblay JP, Skuk D, Rouger K. Human MuStem cells are competent to fuse with nonhuman primate myofibers in a clinically relevant transplantation context: A proof-of-concept study. J Neuropathol Exp Neurol 2024; 83:684-694. [PMID: 38752570 DOI: 10.1093/jnen/nlae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024] Open
Abstract
We previously reported that human muscle-derived stem cells (hMuStem cells) contribute to tissue repair after local administration into injured skeletal muscle or infarcted heart in immunodeficient rodent models. However, extrapolation of these findings to a clinical context is problematic owing to the considerable differences often seen between in vivo findings in humans versus rodents. Therefore, we investigated whether the muscle regenerative behavior of hMuStem cells is maintained in a clinically relevant transplantation context. Human MuStem cells were intramuscularly administered by high-density microinjection matrices into nonhuman primates receiving tacrolimus-based immunosuppression thereby reproducing the protocol that has so far produced the best results in clinical trials of cell therapy in myopathies. Four and 9 weeks after administration, histological analysis of cell injection sites revealed large numbers of hMuStem cell-derived nuclei in all cases. Most graft-derived nuclei were distributed in small myofiber groups in which no signs of a specific immune response were observed. Importantly, hMuStem cells contributed to simian tissue repair by fusing mainly with host myofibers, demonstrating their capacity for myofiber regeneration in this model. Together, these findings obtained in a valid preclinical model provide new insights supporting the potential of hMuStem cells in future cell therapies for muscle diseases.
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Affiliation(s)
- Marine Charrier
- Oniris, INRAE, PAnTher, Nantes, France
- L'institut du Thorax, INSERM, CNRS, UNIV Nantes, Nantes, France
- Nantes Université, Nantes, France
| | | | | | | | | | - Antoine Hamel
- Service de Chirurgie Infantile, Centre Hospitalier Universitaire (CHU) de Nantes, Nantes, France
| | - Armelle Magot
- Centre de Référence Maladies Neuromusculaires AOC, Filnemus, Euro-NMD, Laboratoire d'Explorations Fonctionnelles, Centre Hospitalier Universitaire Hôtel Dieu, Nantes, France
| | - Yann Péréon
- Centre de Référence Maladies Neuromusculaires AOC, Filnemus, Euro-NMD, Laboratoire d'Explorations Fonctionnelles, Centre Hospitalier Universitaire Hôtel Dieu, Nantes, France
| | | | - Jacques P Tremblay
- Axe Neurosciences, Research Center of the CHU de Quebec-CHUL and Department of Molecular Medicine, School of Medicine, Laval University, Quebec, Quebec, Canada
| | - Daniel Skuk
- Axe Neurosciences, Research Center of the CHU de Quebec-CHUL and Department of Molecular Medicine, School of Medicine, Laval University, Quebec, Quebec, Canada
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2
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Chen N, Xia X, Hanif Q, Zhang F, Dang R, Huang B, Lyu Y, Luo X, Zhang H, Yan H, Wang S, Wang F, Chen J, Guan X, Liu Y, Li S, Jin L, Wang P, Sun L, Zhang J, Liu J, Qu K, Cao Y, Sun J, Liao Y, Xiao Z, Cai M, Mu L, Siddiki AZ, Asif M, Mansoor S, Babar ME, Hussain T, Silva GLLP, Gorkhali NA, Terefe E, Belay G, Tijjani A, Zegeye T, Gebre MG, Ma Y, Wang Y, Huang Y, Lan X, Chen H, Migliore NR, Colombo G, Semino O, Achilli A, Sinding MHS, Lenstra JA, Cheng H, Lu W, Hanotte O, Han J, Jiang Y, Lei C. Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing. Nat Commun 2023; 14:7803. [PMID: 38016956 PMCID: PMC10684552 DOI: 10.1038/s41467-023-43626-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/14/2023] [Indexed: 11/30/2023] Open
Abstract
Indicine cattle, also referred to as zebu (Bos taurus indicus), play a central role in pastoral communities across a wide range of agro-ecosystems, from extremely hot semiarid regions to hot humid tropical regions. However, their adaptive genetic changes following their dispersal into East Asia from the Indian subcontinent have remained poorly documented. Here, we characterize their global genetic diversity using high-quality whole-genome sequencing data from 354 indicine cattle of 57 breeds/populations, including major indicine phylogeographic groups worldwide. We reveal their probable migration into East Asia was along a coastal route rather than inland routes and we detected introgression from other bovine species. Genomic regions carrying morphology-, immune-, and heat-tolerance-related genes underwent divergent selection according to Asian agro-ecologies. We identify distinct sets of loci that contain promising candidate variants for adaptation to hot semi-arid and hot humid tropical ecosystems. Our results indicate that the rapid and successful adaptation of East Asian indicine cattle to hot humid environments was promoted by localized introgression from banteng and/or gaur. Our findings provide insights into the history and environmental adaptation of indicine cattle.
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Affiliation(s)
- Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiaoting Xia
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, 38000, Pakistan
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), 100193, Beijing, China
| | - Fengwei Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, 650212, China
| | - Yang Lyu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiaoyu Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Hucai Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environment Science, Yunnan University, Kunming, 650500, China
| | - Huixuan Yan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Shikang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Fuwen Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Jialei Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiwen Guan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yangkai Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Shuang Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Liangliang Jin
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Pengfei Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Luyang Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Jicai Zhang
- Yunnan Academy of Grassland and Animal Science, Kunming, 650212, China
| | - Jianyong Liu
- Yunnan Academy of Grassland and Animal Science, Kunming, 650212, China
| | - Kaixing Qu
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong, 675000, China
| | - Yanhong Cao
- Guangxi Vocational University of Agriculture, Nanning, 530007, China
| | - Junli Sun
- Guangxi Vocational University of Agriculture, Nanning, 530007, China
| | - Yuying Liao
- Guangxi Veterinary Research Institute, Guangxi Key Laboratory of Veterinary Biotechnology, Nanning, 530001, China
| | - Zhengzhong Xiao
- Guangxi Vocational University of Agriculture, Nanning, 530007, China
| | - Ming Cai
- Yunnan Academy of Grassland and Animal Science, Kunming, 650212, China
| | - Lan Mu
- College of Landscape and Horticulture, Southwest Forestry University, Kunming, 650224, China
| | - Amam Zonaed Siddiki
- Genomics Research Group, Department of Pathology and Parasitology, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University (CVASU), Chattogram, 4225, Bangladesh
| | - Muhammad Asif
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, 38000, Pakistan
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, 38000, Pakistan
| | - Masroor Ellahi Babar
- The University of Agriculture, Dera Ismail Khan, Khyber Pakhtunkhwa, 29050, Pakistan
| | - Tanveer Hussain
- Department of Molecular Biology, Virtual University of Pakistan, Islamabad, 44100, Pakistan
| | | | - Neena Amatya Gorkhali
- National Animal Breeding and Genetics Centre, National Animal Science Research Institute, Nepal Agriculture Research Council, Khumaltar, Lalitpur, 45200, Nepal
| | - Endashaw Terefe
- College of Agriculture and Environmental Science, Department of Animal Science, Arsi University, Asella, Ethiopia
- International Livestock Research Institute (ILRI), P.O. Box 5689, 1000, Addis Ababa, Ethiopia
| | - Gurja Belay
- College of Natural and Computational Sciences, The School of Graduate Studies, Addis Ababa University, 1000, Addis Ababa, Ethiopia
| | - Abdulfatai Tijjani
- International Livestock Research Institute (ILRI), P.O. Box 5689, 1000, Addis Ababa, Ethiopia
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | - Tsadkan Zegeye
- Mekelle Agricultural Research Center, P.O. Box 258, 7000, Mekelle, Tigray, Ethiopia
| | - Mebrate Genet Gebre
- School of Animal and Rangeland Science, College of Agriculture, Haramaya University, 2040, Haramaya, Oromia, Ethiopia
| | - Yun Ma
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, 750000, China
| | - Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Nicola Rambaldi Migliore
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Giulia Colombo
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Ornella Semino
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Alessandro Achilli
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Mikkel-Holger S Sinding
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, DK-1350, Copenhagen, Denmark
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, 3584 CM, Utrecht, The Netherlands
| | - Haijian Cheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Shandong Key Lab of Animal Disease Control and Breeding, Jinan, 250100, China
| | - Wenfa Lu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Olivier Hanotte
- International Livestock Research Institute (ILRI), P.O. Box 5689, 1000, Addis Ababa, Ethiopia.
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Jianlin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), 100193, Beijing, China.
- Livestock Genetics Program, International Livestock Research Institute (ILRI), 00100, Nairobi, Kenya.
- Yazhouwan National Laboratory, Sanya, 572024, China.
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, 712100, China.
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
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3
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von Seth J, Dussex N, Díez-Del-Molino D, van der Valk T, Kutschera VE, Kierczak M, Steiner CC, Liu S, Gilbert MTP, Sinding MHS, Prost S, Guschanski K, Nathan SKSS, Brace S, Chan YL, Wheat CW, Skoglund P, Ryder OA, Goossens B, Götherström A, Dalén L. Genomic insights into the conservation status of the world's last remaining Sumatran rhinoceros populations. Nat Commun 2021; 12:2393. [PMID: 33896938 PMCID: PMC8071806 DOI: 10.1038/s41467-021-22386-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 03/01/2021] [Indexed: 02/02/2023] Open
Abstract
Small populations are often exposed to high inbreeding and mutational load that can increase the risk of extinction. The Sumatran rhinoceros was widespread in Southeast Asia, but is now restricted to small and isolated populations on Sumatra and Borneo, and most likely extinct on the Malay Peninsula. Here, we analyse 5 historical and 16 modern genomes from these populations to investigate the genomic consequences of the recent decline, such as increased inbreeding and mutational load. We find that the Malay Peninsula population experienced increased inbreeding shortly before extirpation, which possibly was accompanied by purging. The populations on Sumatra and Borneo instead show low inbreeding, but high mutational load. The currently small population sizes may thus in the near future lead to inbreeding depression. Moreover, we find little evidence for differences in local adaptation among populations, suggesting that future inbreeding depression could potentially be mitigated by assisted gene flow among populations.
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Affiliation(s)
- Johanna von Seth
- Centre for Palaeogenetics, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
- Department of Zoology, Stockholm University, Stockholm, Sweden.
| | - Nicolas Dussex
- Centre for Palaeogenetics, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
- Department of Zoology, Stockholm University, Stockholm, Sweden.
| | - David Díez-Del-Molino
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Tom van der Valk
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
| | - Verena E Kutschera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Marcin Kierczak
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Cynthia C Steiner
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, Escondido, CA, USA
| | - Shanlin Liu
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Norwegian University of Science and Technology, University Museum, Trondheim, Norway
| | - Mikkel-Holger S Sinding
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Stefan Prost
- LOEWE-Centre for Translational Biodiversity Genomics, Senckenberg, Frankfurt, Germany
- South African National Biodiversity Institute, National Zoological Garden, Pretoria, South Africa
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Yvonne L Chan
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | | | | | - Oliver A Ryder
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, Escondido, CA, USA
| | - Benoit Goossens
- Sabah Wildlife Department, Kota Kinabalu, Sabah, Malaysia
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff, UK
- Sustainable Places Research Institute, Cardiff University, Cardiff, UK
- Danau Girang Field Centre, c/o Sabah Wildlife Department, Kota Kinabalu, Sabah, Malaysia
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
- Department of Zoology, Stockholm University, Stockholm, Sweden.
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4
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Tsuchiya MTN, Dikow RB, Koepfli KP, Frandsen PB, Rockwood LL, Maldonado JE. Whole-Genome Sequencing of Procyonids Reveals Distinct Demographic Histories in Kinkajou (Potos flavus) and Northern Raccoon (Procyon lotor). Genome Biol Evol 2020; 13:6040737. [PMID: 33331895 PMCID: PMC7851585 DOI: 10.1093/gbe/evaa255] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2020] [Indexed: 01/20/2023] Open
Abstract
Here, we present the initial comparison of the nuclear genomes of the North American raccoon (Procyon lotor) and the kinkajou (Potos flavus) based on draft assemblies. These two species encompass almost 21 Myr of evolutionary history within Procyonidae. Because assemblies greatly impact downstream results, such as gene prediction and annotation, we tested three de novo assembly strategies (implemented in ALLPATHS-LG, MaSuRCA, and Platanus), some of which are optimized for highly heterozygous genomes. We discovered significant variation in contig and scaffold N50 and L50 statistics and genome completeness depending on the de novo assembler used. We compared the performance of these three assembly algorithms in hopes that this study will aid others looking to improve the quality of existing draft genome assemblies even without additional sequence data. We also estimate the demographic histories of raccoons and kinkajous using the Pairwise Sequentially Markovian Coalescent and discuss the variation in population sizes with respect to climatic change during the Pleistocene, as well as aspects of their ecology and taxonomy. Our goal is to achieve a better understanding of the evolutionary history of procyonids and to create robust genomic resources for future studies regarding adaptive divergence and selection.
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Affiliation(s)
- Mirian T N Tsuchiya
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC, USA.,Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | - Rebecca B Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC, USA
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason Univeristy, Front Royal, VA, USA.,Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC, USA
| | - Paul B Frandsen
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC, USA.,Department of Plant & Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Larry L Rockwood
- Department of Biology, George Mason University, Fairfax, VA, USA
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA.,Department of Biology, George Mason University, Fairfax, VA, USA
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Silva P, Galaverni M, Ortega-Del Vecchyo D, Fan Z, Caniglia R, Fabbri E, Randi E, Wayne R, Godinho R. Genomic evidence for the Old divergence of Southern European wolf populations. Proc Biol Sci 2020; 287:20201206. [PMID: 32693716 PMCID: PMC7423677 DOI: 10.1098/rspb.2020.1206] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The grey wolf (Canis lupus) is one of the most widely distributed mammals in which a variety of distinct populations have been described. However, given their currently fragmented distribution and recent history of human-induced population decline, little is known about the events that led to their differentiation. Based on the analysis of whole canid genomes, we examined the divergence times between Southern European wolf populations and their ancient demographic history. We found that all present-day Eurasian wolves share a common ancestor ca 36 000 years ago, supporting the hypothesis that all extant wolves derive from a single population that subsequently expanded after the Last Glacial Maximum. We also estimated that the currently isolated European populations of the Iberian Peninsula, Italy and the Dinarics-Balkans diverged very closely in time, ca 10 500 years ago, and maintained negligible gene flow ever since. This indicates that the current genetic and morphological distinctiveness of Iberian and Italian wolves can be attributed to their isolation dating back to the end of the Pleistocene, predating the recent human-induced extinction of wolves in Central Europe by several millennia.
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Affiliation(s)
- Pedro Silva
- CIBIO/InBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Marco Galaverni
- Conservation Unit, WWF Italia, Via Po 25/c - 00198 Roma, Italy
| | - Diego Ortega-Del Vecchyo
- International Laboratory for Human Genome Research, National Autonomous University of Mexico, Santiago de Querétaro, Querétaro 76230, Mexico
| | - Zhenxin Fan
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Romolo Caniglia
- Unit for Conservation Genetics (BIO-CGE), Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Italian Institute for Environmental Protection and Research (ISPRA), Via Cà Fornacetta 9, 40064 Ozzano dell'Emilia (Bo), Italy
| | - Elena Fabbri
- Unit for Conservation Genetics (BIO-CGE), Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Italian Institute for Environmental Protection and Research (ISPRA), Via Cà Fornacetta 9, 40064 Ozzano dell'Emilia (Bo), Italy
| | - Ettore Randi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Selmi 3, Bologna 40126, Italy.,Department of Chemistry and Bioscience, Faculty of Engineering and Science, University of Aalborg, Aalborg, Denmark
| | - Robert Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Raquel Godinho
- CIBIO/InBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal.,Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland Park 2006, South Africa
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6
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Upperman LR, Kinghorn BP, MacNeil MD, Van Eenennaam AL. Management of lethal recessive alleles in beef cattle through the use of mate selection software. Genet Sel Evol 2019; 51:36. [PMID: 31382878 PMCID: PMC6683482 DOI: 10.1186/s12711-019-0477-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 06/18/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Recessive loss-of-function (LOF) alleles at genes which are essential for life, can result in early embryonic mortality. Cattle producers can use the LOF carrier status of individual animals to make selection and mate allocation decisions. METHODS Two beef cattle breeding strategies i.e. (1) selection against LOF carriers as parents and (2) simultaneous selection and mate allocation to avoid the occurrence of homozygous offspring in three scenarios, which differed in number and frequency of LOF alleles were evaluated using the mate selection program, MateSel. Scenarios included (a) seven loci with high-frequency LOF alleles, (b) 76 loci with low-frequency LOF alleles, and (c) 50 loci with random high- and low-frequency LOF alleles. In addition, any savings resulting from the information obtained by varying the percentage (0-100%) of the herd genotyped, together with segregation analysis to cover ungenotyped animals, were calculated to determine (1) which percentage optimized net profit for a fixed cost of genotyping ($30/test), and (2) the breakeven cost for genotyping. RESULTS With full knowledge of the LOF alleles carried by selection candidates, the most profitable breeding strategy was always simultaneous selection and mate allocation to avoid homozygous affected offspring (aa) as compared to indiscriminate selection against carrier parents (Aa). The breakeven value of genotyping depended on the number of loci modeled, the LOF allele frequencies, and the mating/selection strategies used. Genotyping was most valuable when it was used to avoid otherwise high levels of embryonic mortalities. As the number of essential loci with LOF alleles increased, especially when some were present at relatively high minor allele frequencies, embryonic losses increased, and profit was maximized by genotyping 10 to 20% of a herd and using that information to reduce these losses. CONCLUSIONS Genotyping 100% of the herd was never the most profitable outcome in any scenario; however, genotyping some proportion of the herd, together with segregation analysis to cover ungenotyped animals, maximized overall profit in scenarios with large numbers of loci with LOF alleles. As more LOF alleles are identified, such a mate selection software will likely be required to optimally select and allocate matings to balance the rate of genetic gain, embryonic losses, and inbreeding.
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Affiliation(s)
- Lindsay R. Upperman
- Department of Animal Science, University of California, Davis, CA 95616 USA
- Present Address: Department of Animal Science, University of Nebraska, Lincoln, NE 68583 USA
| | - Brian P. Kinghorn
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351 Australia
| | - Michael D. MacNeil
- Delta G, Miles City, MT 59301 USA
- University of the Free State, Bloemfontein, 9300 South Africa
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7
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Rakotoarivelo AR, O’Donoghue P, Bruford MW, Moodley Y. An ancient hybridization event reconciles mito-nuclear discordance among spiral-horned antelopes. J Mammal 2019. [DOI: 10.1093/jmammal/gyz089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Abstract
The spiral-horned antelopes (genus Tragelaphus) are among the most phenotypically diverse of all large mammals, and evolved in Africa during an adaptive radiation that began in the late Miocene, around 6 million years ago. Tragelaphus was able to exploit the habitat heterogeneity created by Plio-Pleistocene paleoclimatic fluctuations and tectonic processes to eventually occupy almost every habitat type in present day sub-Saharan Africa. The smallest of the spiral-horned antelopes, the bushbuck (T. scriptus), is also widely distributed across Africa, but is genetically divided into polyphyletic Scriptus and Sylvaticus mitochondrial (mt)DNA superlineages that inhabit opposite halves of the continent, suggesting the convergent evolution of independent bushbuck species. In this study, we provide a species tree reconstruction for the genus Tragelaphus and show that Scriptus and Sylvaticus are reciprocally monophyletic at nuclear DNA loci, comprising a single species across its African range. Given that mtDNA will sort into species-specific lineages more quickly than nuclear DNA, only an ancient interspecific hybridization event between a female from a now-extinct Tragelaphus species and a proto-Scriptus bushbuck male can reconcile the mito-nuclear incongruence. This extinct species diverged from the nyala (T. angasii) in the Pliocene about 4.1 million years ago. This study adds to an increasing body of evidence that suggests interspecific hybridization may be more common than previously thought.
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Affiliation(s)
- Andrinajoro R Rakotoarivelo
- Department of Zoology, University of Venda, Thohoyandou, Republic of South Africa
- Natiora Ahy, Lot Bis, Ampahibe, Antananarivo, Madagascar
| | | | - Michael W Bruford
- Cardiff School of Biosciences, Sir Martin Evans Building, Cardiff University, Museum Avenue, Cardiff, United Kingdom
| | - Yoshan Moodley
- Department of Zoology, University of Venda, Thohoyandou, Republic of South Africa
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8
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The Evolution and Population Diversity of Bison in Pleistocene and Holocene Eurasia: Sex Matters. DIVERSITY 2018. [DOI: 10.3390/d10030065] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Knowledge about the origin and evolutionary history of the bison has been improved recently owing to several genomic and paleogenomic studies published in the last two years, which elucidated large parts of the evolution of bison populations during the Upper Pleistocene and Holocene in Eurasia. The produced data, however, were interpreted in contradicting manners. Here, we have gathered, reanalyzed and compared previously published or unpublished morphometric and genetic data that have not yet been integrated and that we synthesize in a unified framework. In particular, we re-estimate dates of divergence of mitogenome lineages based on an extended dataset comprising 81 complete ancient bison mitogenomes and we revisit putative gene flow between the Bos and Bison genera based on comparative analyses of ancient and modern bison genomes, thereby questioning published conclusions. Morphometric analyses taking into account sexual dimorphism invalidate a previous claim that Bison schoetensacki was present in France during the Late Pleistocene. Both morphometric and genome analyses reveal that Eurasian bison belonging to different Bison priscus and Bison bonasus lineages maintained parallel evolutionary paths with gene flow during a long period of incomplete speciation that ceased only upon the migration of B. priscus to the American continent establishing the American bison lineage. Our nuclear genome analysis of the evolutionary history of B. bonasus allows us to reject the previous hypothesis that it is a hybrid of B. priscus and Bos primigenius. Based on present-day behavioral studies of European and American bison, we propose that apparently conflicting lines of evidence can be reconciled by positing that female bison drove the specialization of bison populations to different ecological niches while male bison drove regular homogenizing genetic exchanges between populations.
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Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia. Nat Commun 2018; 9:2337. [PMID: 29904051 PMCID: PMC6002414 DOI: 10.1038/s41467-018-04737-0] [Citation(s) in RCA: 190] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 05/10/2018] [Indexed: 02/07/2023] Open
Abstract
Cattle domestication and the complex histories of East Asian cattle breeds warrant further investigation. Through analysing the genomes of 49 modern breeds and eight East Asian ancient samples, worldwide cattle are consistently classified into five continental groups based on Y-chromosome haplotypes and autosomal variants. We find that East Asian cattle populations are mainly composed of three distinct ancestries, including an earlier East Asian taurine ancestry that reached China at least ~3.9 kya, a later introduced Eurasian taurine ancestry, and a novel Chinese indicine ancestry that diverged from Indian indicine approximately 36.6–49.6 kya. We also report historic introgression events that helped domestic cattle from southern China and the Tibetan Plateau achieve rapid adaptation by acquiring ~2.93% and ~1.22% of their genomes from banteng and yak, respectively. Our findings provide new insights into the evolutionary history of cattle and the importance of introgression in adaptation of cattle to new environmental challenges in East Asia. There are various indigenous cattle breeds in East Asia which have a complex history. Here, the authors analyse the genomes of 49 modern breeds and eight ancient samples and identify three distinct ancestries and multiple adaptive introgressions from other bovine species.
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10
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Mays HL, Hung CM, Shaner PJ, Denvir J, Justice M, Yang SF, Roth TL, Oehler DA, Fan J, Rekulapally S, Primerano DA. Genomic Analysis of Demographic History and Ecological Niche Modeling in the Endangered Sumatran Rhinoceros Dicerorhinus sumatrensis. Curr Biol 2017; 28:70-76.e4. [PMID: 29249659 DOI: 10.1016/j.cub.2017.11.021] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/11/2017] [Accepted: 11/07/2017] [Indexed: 12/30/2022]
Abstract
The vertebrate extinction rate over the past century is approximately 22-100 times greater than background extinction rates [1], and large mammals are particularly at risk [2, 3]. Quaternary megafaunal extinctions have been attributed to climate change [4], overexploitation [5], or a combination of the two [6]. Rhinoceroses (Family: Rhinocerotidae) have a rich fossil history replete with iconic examples of climate-induced extinctions [7], but current pressures threaten to eliminate this group entirely. The Sumatran rhinoceros (Dicerorhinus sumatrensis) is among the most imperiled mammals on earth. The 2011 population was estimated at ≤216 wild individuals [8], and currently the species is extirpated, or nearly so, throughout the majority of its former range [8-12]. Understanding demographic history is important in placing current population status into a broader ecological and evolutionary context. Analysis of the Sumatran rhinoceros genome reveals extreme changes in effective population size throughout the Pleistocene. Population expansion during the early to middle Pleistocene was followed by decline. Ecological niche modeling indicated that changing climate most likely played a role in the decline of the Sumatran rhinoceros, as less suitable habitat on an emergent Sundaland corridor isolated Sumatran rhinoceros populations. By the end of the Pleistocene, the Sundaland corridor was submerged, and populations were fragmented and consequently reduced to low Holocene levels from which they would never recover. Past events denuded the Sumatran rhinoceros of genetic diversity through population decline, fragmentation, or some combination of the two and most likely made the species even more susceptible to later exploitation and habitat loss. VIDEO ABSTRACT.
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Affiliation(s)
- Herman L Mays
- Marshall University, Department of Biological Sciences, Huntington, WV 25755, USA; Cincinnati Museum Center, Cincinnati, OH 45203, USA.
| | - Chih-Ming Hung
- Academia Sinica, Biodiversity Research Center, Taipei 11529, Taiwan
| | - Pei-Jen Shaner
- National Taiwan Normal University, Department of Life Sciences, Taipei 116, Taiwan
| | - James Denvir
- Marshall University, Department of Biomedical Sciences, Huntington, WV 25755, USA
| | - Megan Justice
- Marshall University, Department of Biomedical Sciences, Huntington, WV 25755, USA
| | - Shang-Fang Yang
- Academia Sinica, Biodiversity Research Center, Taipei 11529, Taiwan
| | - Terri L Roth
- Cincinnati Zoo and Botanical Garden, Center for Conservation and Research of Endangered Wildlife, Cincinnati, OH 45220, USA
| | - David A Oehler
- Wildlife Conservation Society, Bronx Zoo, New York, NY 10460, USA
| | - Jun Fan
- Marshall University, Department of Biomedical Sciences, Huntington, WV 25755, USA
| | | | - Donald A Primerano
- Marshall University, Department of Biomedical Sciences, Huntington, WV 25755, USA
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Gautier M, Moazami-Goudarzi K, Levéziel H, Parinello H, Grohs C, Rialle S, Kowalczyk R, Flori L. Deciphering the Wisent Demographic and Adaptive Histories from Individual Whole-Genome Sequences. Mol Biol Evol 2016; 33:2801-2814. [PMID: 27436010 PMCID: PMC5062319 DOI: 10.1093/molbev/msw144] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
As the largest European herbivore, the wisent (Bison bonasus) is emblematic of the continent wildlife but has unclear origins. Here, we infer its demographic and adaptive histories from two individual whole-genome sequences via a detailed comparative analysis with bovine genomes. We estimate that the wisent and bovine species diverged from 1.7 × 106 to 850,000 years before present (YBP) through a speciation process involving an extended period of limited gene flow. Our data further support the occurrence of more recent secondary contacts, posterior to the Bos taurus and Bos indicus divergence (∼150,000 YBP), between the wisent and (European) taurine cattle lineages. Although the wisent and bovine population sizes experienced a similar sharp decline since the Last Glacial Maximum, we find that the wisent demography remained more fluctuating during the Pleistocene. This is in agreement with a scenario in which wisents responded to successive glaciations by habitat fragmentation rather than southward and eastward migration as for the bovine ancestors. We finally detect 423 genes under positive selection between the wisent and bovine lineages, which shed a new light on the genome response to different living conditions (temperature, available food resource, and pathogen exposure) and on the key gene functions altered by the domestication process.
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Affiliation(s)
- Mathieu Gautier
- CBGP, INRA, CIRAD, IRD, Supagro, Montferrier-sur-Lez, France IBC, Institut de Biologie Computationnelle, Montpellier, France
| | | | | | - Hugues Parinello
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, Montpellier, France
| | - Cécile Grohs
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Stéphanie Rialle
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, Montpellier, France
| | - Rafał Kowalczyk
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Laurence Flori
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France INTERTRYP, CIRAD, IRD, Montpellier, France
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12
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13
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Wang GD, Zhai W, Yang HC, Wang L, Zhong L, Liu YH, Fan RX, Yin TT, Zhu CL, Poyarkov AD, Irwin DM, Hytönen MK, Lohi H, Wu CI, Savolainen P, Zhang YP. Out of southern East Asia: the natural history of domestic dogs across the world. Cell Res 2016; 26:21-33. [PMID: 26667385 PMCID: PMC4816135 DOI: 10.1038/cr.2015.147] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 09/09/2015] [Accepted: 10/10/2015] [Indexed: 12/30/2022] Open
Abstract
The origin and evolution of the domestic dog remains a controversial question for the scientific community, with basic aspects such as the place and date of origin, and the number of times dogs were domesticated, open to dispute. Using whole genome sequences from a total of 58 canids (12 gray wolves, 27 primitive dogs from Asia and Africa, and a collection of 19 diverse breeds from across the world), we find that dogs from southern East Asia have significantly higher genetic diversity compared to other populations, and are the most basal group relating to gray wolves, indicating an ancient origin of domestic dogs in southern East Asia 33 000 years ago. Around 15 000 years ago, a subset of ancestral dogs started migrating to the Middle East, Africa and Europe, arriving in Europe at about 10 000 years ago. One of the out of Asia lineages also migrated back to the east, creating a series of admixed populations with the endemic Asian lineages in northern China before migrating to the New World. For the first time, our study unravels an extraordinary journey that the domestic dog has traveled on earth.
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Affiliation(s)
- Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Weiwei Zhai
- Human Genetics, Genome Institute of Singapore, A*STAR, 60 Biopolis Street, Genome #02-01, Singapore 138672, Singapore
| | - He-Chuan Yang
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Human Genetics, Genome Institute of Singapore, A*STAR, 60 Biopolis Street, Genome #02-01, Singapore 138672, Singapore
- Department of Molecular and Cell Biology, School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Lu Wang
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
| | - Li Zhong
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
| | - Yan-Hu Liu
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
| | - Ruo-Xi Fan
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650223, China
| | - Chun-Ling Zhu
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Andrei D Poyarkov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Science, 33 Leninskiy Prospect, Moscow 119071, Russia
| | - David M Irwin
- Laboratory Medicine & Pathobiology, University of Toronto, 1 King's College Circle, Rm 6211, Toronto, ON, Canada M5S 1A8
| | - Marjo K Hytönen
- Research Programs Unit, Molecular Neurology and Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, Helsinki, Finland
| | - Hannes Lohi
- Research Programs Unit, Molecular Neurology and Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, Helsinki, Finland
| | - Chung-I Wu
- Department of Ecology and Evolution, University of Chicago, 5801 S Ellis Ave, Chicago, IL 60637, USA
| | - Peter Savolainen
- Department of Gene Technology, KTH-Royal Institute of Technology, Science for Life Laboratory, Tomtebodavägen 23A, 17165 Solna, Sweden
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Laboratory for Conservation and Utilization of Bio-resource & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
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Skuk D, Tremblay JP. Cell therapy in muscular dystrophies: many promises in mice and dogs, few facts in patients. Expert Opin Biol Ther 2015; 15:1307-19. [PMID: 26076715 DOI: 10.1517/14712598.2015.1057564] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Muscular dystrophies (MDs) are genetic diseases that produce progressive loss of skeletal muscle fibers. Cell therapy (CT) is an experimental approach to treat MD. The first clinical trials of CT in MD conducted in the 1990s were based on myoblast transplantation (MT). Since they did not yield the expected results, several researchers sought to discover other cells with more advantageous properties than myoblasts whereas others sought to improve MT. AREAS COVERED We explain the properties that are required for a cell to be used in CT of MD. We briefly review most of the cells that were proposed for this CT, and to what extent these properties were met not only in laboratory animals but also in clinical trials. EXPERT OPINION Although the repertoire of cells proposed for CT of MD has been expanded since the 1990s, only myoblasts have currently demonstrated unequivocally to significantly engraft in humans. Indeed, MT for MD involves significant technical challenges that need be solved. While it would be ideal to find cells involving less technical challenges for CT of MD, there is so far no clinical evidence that this is possible and therefore the work to improve MT should continue.
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Affiliation(s)
- Daniel Skuk
- Axe Neurosciences, P-09300, Centre Hospitalier de l'Université Laval , 2705 boulevard Laurier, Québec (QC), G1V 4G2 , Canada +1 418 654 2186 ; +1 418 654 2207 ;
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15
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Babarinde IA, Saitou N. Heterogeneous tempo and mode of conserved noncoding sequence evolution among four mammalian orders. Genome Biol Evol 2014; 5:2330-43. [PMID: 24259317 PMCID: PMC3879966 DOI: 10.1093/gbe/evt177] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Conserved noncoding sequences (CNSs) of vertebrates are considered to be closely linked with protein-coding gene regulatory functions. We examined the abundance and genomic distribution of CNSs in four mammalian orders: primates, rodents, carnivores, and cetartiodactyls. We defined the two thresholds for CNS using conservation level of coding genes; using all the three coding positions and using only first and second codon positions. The abundance of CNSs varied among lineages, with primates and rodents having highest and lowest number of CNSs, respectively, whereas carnivores and cetartiodactyls had intermediate values. These CNSs cover 1.3-5.5% of the mammalian genomes and have signatures of selective constraints that are stronger in more ancestral than the recent ones. Evolution of new CNSs as well as retention of ancestral CNSs contribute to the differences in abundance. The genomic distribution of CNSs is dynamic with higher proportions of rodent and primate CNSs located in the introns compared with carnivores and cetartiodactyls. In fact, 19% of orthologous single-copy CNSs between human and dog are located in different genomic regions. If CNSs can be considered as candidates of gene expression regulatory sequences, heterogeneity of CNSs among the four mammalian orders may have played an important role in creating the order-specific phenotypes. Fewer CNSs in rodents suggest that rodent diversity is related to lower regulatory conservation. With CNSs shown to cluster around genes involved in nervous systems and the higher number of primate CNSs, our result suggests that CNSs may be involved in the higher complexity of the primate nervous system.
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Affiliation(s)
- Isaac Adeyemi Babarinde
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima Japan
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16
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Kõks S, Reimann E, Lilleoja R, Lättekivi F, Salumets A, Reemann P, Jaakma Ü. Sequencing and annotated analysis of full genome of Holstein breed bull. Mamm Genome 2014; 25:363-73. [PMID: 24770584 DOI: 10.1007/s00335-014-9511-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Accepted: 03/18/2014] [Indexed: 12/21/2022]
Abstract
In the present study, we describe the deep sequencing and structural analysis of the Holstein breed bull genome. Our aim was to receive a high-quality Holstein bull genome reference sequence and to describe different types of variations in its genome compared to Hereford breed as a reference. We generated four mate-paired libraries and one fragment library from 30 μg of genomic DNA. Colour space fasta were mapped and paired to the reference cow (Bos taurus) genome assembly from Oct. 2011 (Baylor 4.6.1/bosTau7). Initial sequencing resulted in the 4,864,054,296 of 50-bp reads. Average mapping efficiency was 71.7 % and altogether 3,494,534,136 reads and 157,928,163,086 bp were successfully mapped, resulting in 60 × coverage. This is the highest coverage for bovine genome published so far. Tertiary analysis found 6,362,988 SNPs in the bull's genome, 4,045,889 heterozygous and 2,317,099 homozygous variants. Annotation revealed that 4,330,337 of all discovered SNPs were annotated in the dbSNP database (build 137) and therefore 2,032,651 SNPs were novel. Large indel variations accounted for the 245,947,845 bp of the variation in entire genome and their number was 312,879. We also found that small indels (number was 633,310) accounted for the total variation of 2,542,552 nucleotides in the genome. Only 106,768 small indels were listed in the dbSNP. Finally, we identified 2,758 inversions in the genome of the bull covering in total 23,099,054 bp of genome's variation. The largest inversion was 87,440 bp in size. In conclusion, the present study discovered different types of novel variants in bull's genome after high-coverage sequencing. Better knowledge of the functions of these variations is needed.
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Affiliation(s)
- Sulev Kõks
- Department of Reproductive Biology, Estonian University of Life Sciences, Tartu, Estonia,
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17
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Tsai MC, Blelloch G, Ravi R, Schwartz R. Coalescent-based method for learning parameters of admixture events from large-scale genetic variation data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2013; 10:1137-1149. [PMID: 23959633 PMCID: PMC4019315 DOI: 10.1109/tcbb.2013.98] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Detecting and quantifying the timing and the genetic contributions of parental populations to a hybrid population is an important but challenging problem in reconstructing evolutionary histories from genetic variation data. With the advent of high throughput genotyping technologies, new methods suitable for large-scale data are especially needed. Furthermore, existing methods typically assume the assignment of individuals into subpopulations is known, when that itself is a difficult problem often unresolved for real data. Here, we propose a novel method that combines prior work for inferring non reticulate population structures with an MCMC scheme for sampling over admixture scenarios to both identify population assignments and learn divergence times and admixture proportions for those populations using genome-scale admixed genetic variation data. We validated our method using coalescent simulations and a collection of real bovine and human variation data. On simulated sequences, our methods show better accuracy and faster run time than leading competitive methods in estimating admixture fractions and divergence times. Analysis on the real data further shows our methods to be effective at matching our best current knowledge about the relevant populations.
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Affiliation(s)
- Ming-Chi Tsai
- Joint CMU-Pitt PhD Program in Computational Biology, Pittsburgh, PA, 15213.
| | - Guy Blelloch
- Department of Computer Science, Carnegie Mellong University, Pittsburgh, PA 15213.
| | - R. Ravi
- Tepper School of Business, Carnegie Mellon University, Pittsburgh, PA 15213.
| | - Russell Schwartz
- Department of Biological Science, Carnegie Mellon University, Pittsburgh, PA 15213.
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18
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Tarlinton RE, Barfoot HK, Allen CE, Brown K, Gifford RJ, Emes RD. Characterisation of a group of endogenous gammaretroviruses in the canine genome. Vet J 2013; 196:28-33. [DOI: 10.1016/j.tvjl.2012.08.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 08/09/2012] [Accepted: 08/12/2012] [Indexed: 12/25/2022]
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19
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McDonell L, Drouin G. The abundance of processed pseudogenes derived from glycolytic genes is correlated with their expression level. Genome 2012; 55:147-51. [PMID: 22309162 DOI: 10.1139/g2012-002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The abundance of processed pseudogenes in different vertebrate species is known to be proportional to the length of their oogenesis. However, this hypothesis cannot explain why, in a given species, certain genes produce more processed pseudogenes than others. In particular, one would expect that all genes of the glycolytic pathway would generate roughly the same number of processed pseudogenes. However, some glycolitic genes generate more processed pseudogenes than others. Here, we show that there is a positive correlation between the abundance of processed pseudogene generated from glycolytic genes and their level of expression. The variation in expression level of different glycolytic genes likely reflects the fact that some of them, such a GAPDH, have functions other than those they play in glycolysis. Furthermore, the age distribution of GAPDH-processed pseudogenes corresponds to the age distribution of LINE1 elements, which are the source of the reverse transcriptase that generates processed pseudogenes. These results support the hypothesis that gene expression levels affect the level of processed pseudogene production.
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Affiliation(s)
- Laura McDonell
- Département de biologie et Centre de recherche avancée en génomique environnementale, Université d'Ottawa, Ottawa, ON, Canada
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Schmitz J, Brosius J. Exonization of transposed elements: A challenge and opportunity for evolution. Biochimie 2011; 93:1928-34. [PMID: 21787833 DOI: 10.1016/j.biochi.2011.07.014] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 07/11/2011] [Indexed: 10/17/2022]
Abstract
Protein-coding genes are composed of exons and introns flanked by untranslated regions. Before the mRNA of a gene can be translated into protein, the splicing machinery removes all the intronic regions and joins the protein-coding exons together. Exonization is a process, whereby genes acquire new exons from non-protein-coding, primarily intronic, DNA sequences. Genomic insertions or point mutations within DNA sequences often generate alternative splice sites, causing the splicing system to include new sequences as exons or to elongate existing exons. Because the alternative splice sites are not as efficient as the originals the new variants usually constitute a minor fraction of mature mRNAs. While the prevailing original splice variant maintains functionality, the additional sequence, free from selection pressure, evolves a new function or eventually vanishes. If the new splice variant is advantageous, selection might operate to optimize the new splice sites and consequently increase the proportion of the alternative splice variant. In some instances, the original splice variant is completely replaced by constitutive splicing of the new form. Because of the fortuitous presence of internal splice site-like structures within their sequences, portions of transposed elements frequently serve as modules of exonization. Their recruitment requires a long and versatile optimization process involving multiple changes over a time span of millions, even hundreds of millions, of years. Comparisons of corresponding genes and mRNAs in phylogenetically related species enables one to chronologically reconstruct such changes, from ancient ancestors to living species, in a stepwise manner. We will review this process using three different exemplary cases: (1) the evolution of a constitutively spliced mammalian-wide repeat (MIR), (2) the evolution of an alternative exon 1 from an alternative 5'-extended primary transcript containing an Alu element, and (3) a rare case of the stepwise exoniztion of an Alu element-derived sequence mediated by A-to-I RNA editing.
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Affiliation(s)
- Jürgen Schmitz
- Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany.
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Martínez Barrio Á, Ekerljung M, Jern P, Benachenhou F, Sperber GO, Bongcam-Rudloff E, Blomberg J, Andersson G. The first sequenced carnivore genome shows complex host-endogenous retrovirus relationships. PLoS One 2011; 6:e19832. [PMID: 21589882 PMCID: PMC3093408 DOI: 10.1371/journal.pone.0019832] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Accepted: 04/18/2011] [Indexed: 11/25/2022] Open
Abstract
Host-retrovirus interactions influence the genomic landscape and have contributed substantially to mammalian genome evolution. To gain further insights, we analyzed a female boxer (Canis familiaris) genome for complexity and integration pattern of canine endogenous retroviruses (CfERV). Intriguingly, the first such in-depth analysis of a carnivore species identified 407 CfERV proviruses that represent only 0.15% of the dog genome. In comparison, the same detection criteria identified about six times more HERV proviruses in the human genome that has been estimated to contain a total of 8% retroviral DNA including solitary LTRs. These observed differences in man and dog are likely due to different mechanisms to purge, restrict and protect their genomes against retroviruses. A novel group of gammaretrovirus-like CfERV with high similarity to HERV-Fc1 was found to have potential for active retrotransposition and possibly lateral transmissions between dog and human as a result of close interactions during at least 10.000 years. The CfERV integration landscape showed a non-uniform intra- and inter-chromosomal distribution. Like in other species, different densities of ERVs were observed. Some chromosomal regions were essentially devoid of CfERVs whereas other regions had large numbers of integrations in agreement with distinct selective pressures at different loci. Most CfERVs were integrated in antisense orientation within 100 kb from annotated protein-coding genes. This integration pattern provides evidence for selection against CfERVs in sense orientation relative to chromosomal genes. In conclusion, this ERV analysis of the first carnivorous species supports the notion that different mammals interact distinctively with endogenous retroviruses and suggests that retroviral lateral transmissions between dog and human may have occurred.
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Affiliation(s)
- Álvaro Martínez Barrio
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Marie Ekerljung
- Department of Animal Breeding and Genetics, Biomedical Centre, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Patric Jern
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Farid Benachenhou
- Department of Animal Breeding and Genetics, Biomedical Centre, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Section of Virology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Göran O. Sperber
- Department of Neuroscience, Physiology, Uppsala University, Uppsala, Sweden
| | - Erik Bongcam-Rudloff
- Department of Animal Breeding and Genetics, Biomedical Centre, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Jonas Blomberg
- Section of Virology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Göran Andersson
- Department of Animal Breeding and Genetics, Biomedical Centre, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail:
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Liu GE, Ventura M, Cellamare A, Chen L, Cheng Z, Zhu B, Li C, Song J, Eichler EE. Analysis of recent segmental duplications in the bovine genome. BMC Genomics 2009; 10:571. [PMID: 19951423 PMCID: PMC2796684 DOI: 10.1186/1471-2164-10-571] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Accepted: 12/01/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Duplicated sequences are an important source of gene innovation and structural variation within mammalian genomes. We performed the first systematic and genome-wide analysis of segmental duplications in the modern domesticated cattle (Bos taurus). Using two distinct computational analyses, we estimated that 3.1% (94.4 Mb) of the bovine genome consists of recently duplicated sequences (>or= 1 kb in length, >or= 90% sequence identity). Similar to other mammalian draft assemblies, almost half (47% of 94.4 Mb) of these sequences have not been assigned to cattle chromosomes. RESULTS In this study, we provide the first experimental validation large duplications and briefly compared their distribution on two independent bovine genome assemblies using fluorescent in situ hybridization (FISH). Our analyses suggest that the (75-90%) of segmental duplications are organized into local tandem duplication clusters. Along with rodents and carnivores, these results now confidently establish tandem duplications as the most likely mammalian archetypical organization, in contrast to humans and great ape species which show a preponderance of interspersed duplications. A cross-species survey of duplicated genes and gene families indicated that duplication, positive selection and gene conversion have shaped primates, rodents, carnivores and ruminants to different degrees for their speciation and adaptation. We identified that bovine segmental duplications corresponding to genes are significantly enriched for specific biological functions such as immunity, digestion, lactation and reproduction. CONCLUSION Our results suggest that in most mammalian lineages segmental duplications are organized in a tandem configuration. Segmental duplications remain problematic for genome and assembly and we highlight genic regions that require higher quality sequence characterization. This study provides insights into mammalian genome evolution and generates a valuable resource for cattle genomics research.
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Affiliation(s)
- George E Liu
- USDA, ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville, Maryland 20705, USA.
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Shepelev VA, Alexandrov AA, Yurov YB, Alexandrov IA. The evolutionary origin of man can be traced in the layers of defunct ancestral alpha satellites flanking the active centromeres of human chromosomes. PLoS Genet 2009; 5:e1000641. [PMID: 19749981 PMCID: PMC2729386 DOI: 10.1371/journal.pgen.1000641] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Accepted: 08/11/2009] [Indexed: 02/01/2023] Open
Abstract
Alpha satellite domains that currently function as centromeres of human chromosomes are flanked by layers of older alpha satellite, thought to contain dead centromeres of primate progenitors, which lost their function and the ability to homogenize satellite repeats, upon appearance of a new centromere. Using cladistic analysis of alpha satellite monomers, we elucidated complete layer patterns on chromosomes 8, 17, and X and related them to each other and to primate alpha satellites. We show that discrete and chronologically ordered alpha satellite layers are partially symmetrical around an active centromere and their succession is partially shared in non-homologous chromosomes. The layer structure forms a visual representation of the human evolutionary lineage with layers corresponding to ancestors of living primates and to entirely fossil taxa. Surprisingly, phylogenetic comparisons suggest that alpha satellite arrays went through periods of unusual hypermutability after they became "dead" centromeres. The layer structure supports a model of centromere evolution where new variants of a satellite repeat expanded periodically in the genome by rounds of inter-chromosomal transfer/amplification. Each wave of expansion covered all or many chromosomes and corresponded to a new primate taxon. Complete elucidation of the alpha satellite phylogenetic record would give a unique opportunity to number and locate the positions of major extinct taxa in relation to human ancestors shared with extant primates. If applicable to other satellites in non-primate taxa, analysis of centromeric layers could become an invaluable tool for phylogenetic studies.
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Affiliation(s)
- Valery A. Shepelev
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | | | - Yuri B. Yurov
- Mental Health Research Centre, Russian Academy of Medical Sciences, Moscow, Russia
| | - Ivan A. Alexandrov
- Mental Health Research Centre, Russian Academy of Medical Sciences, Moscow, Russia
- * E-mail:
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Adelson DL, Raison JM, Edgar RC. Characterization and distribution of retrotransposons and simple sequence repeats in the bovine genome. Proc Natl Acad Sci U S A 2009; 106:12855-60. [PMID: 19625614 PMCID: PMC2722308 DOI: 10.1073/pnas.0901282106] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2009] [Indexed: 12/11/2022] Open
Abstract
Interspersed repeat composition and distribution in mammals have been best characterized in the human and mouse genomes. The bovine genome contains typical eutherian mammal repeats, but also has a significant number of long interspersed nuclear element RTE (BovB) elements proposed to have been horizontally transferred from squamata. Our analysis of the BovB repeats has indicated that only a few of them are currently likely to retrotranspose in cattle. However, bovine L1 repeats (L1 BT) have many likely active copies. Comparison of substitution rates for BovB and L1 BT indicates that L1 BT is a younger repeat family than BovB. In contrast to mouse and human, L1 occurrence is not negatively correlated with G+C content. However, BovB, Bov A2, ART2A, and Bov-tA are negatively correlated with G+C, although Bov-tAs correlation is weaker. Also, by performing genome wide correlation analysis of interspersed and simple sequence repeats, we have identified genome territories by repeat content that appear to define ancestral vs. ruminant-specific genomic regions. These ancestral regions, enriched with L2 and MIR repeats, are largely conserved between bovine and human.
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Affiliation(s)
- David L Adelson
- School of Molecular and Biomedical Science, University of Adelaide, North Terrace, Adelaide, South Australia, 5005, Australia.
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25
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Comparative genomics indicates the mammalian CD33rSiglec locus evolved by an ancient large-scale inverse duplication and suggests all Siglecs share a common ancestral region. Immunogenetics 2009; 61:401-17. [PMID: 19337729 DOI: 10.1007/s00251-009-0372-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Accepted: 03/20/2009] [Indexed: 12/27/2022]
Abstract
The CD33-related sialic acid binding Ig-like lectins (CD33rSiglecs) are predominantly inhibitory receptors expressed on leukocytes. They are distinguishable from conserved Siglecs, such as Sialoadhesin and MAG, by their rapid evolution. A comparison of the CD33rSiglec gene cluster in different mammalian species showed that it can be divided into subclusters, A and B. The two subclusters, inverted in relation to each other, each encode a set of CD33rSiglec genes arranged head-to-tail. Two regions of strong correspondence provided evidence for a large-scale inverse duplication, encompassing the framework CEACAM-18 (CE18) and ATPBD3 (ATB3) genes that seeded the mammalian CD33rSiglec cluster. Phylogenetic analysis was consistent with the predicted inversion. Rodents appear to have undergone wholesale loss of CD33rSiglec genes after the inverse duplication. In contrast, CD33rSiglecs expanded in primates and many are now pseudogenes with features consistent with activating receptors. In contrast to mammals, the fish CD33rSiglecs clusters show no evidence of an inverse duplication. They display greater variation in cluster size and structure than mammals. The close arrangement of other Siglecs and CD33rSiglecs in fish is consistent with a common ancestral region for Siglecs. Expansion of mammalian CD33rSiglecs appears to have followed a large inverse duplication of a smaller primordial cluster over 180 million years ago, prior to eutherian/marsupial divergence. Inverse duplications in general could potentially have a stabilizing effect in maintaining the size and structure of large gene clusters, facilitating the rapid evolution of immune gene families.
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26
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Mahler KL, Fleming JL, Dworkin AM, Gladman N, Cho HY, Mao JH, Balmain A, Toland AE. Sequence divergence of Mus spretus and Mus musculus across a skin cancer susceptibility locus. BMC Genomics 2008; 9:626. [PMID: 19105829 PMCID: PMC2628916 DOI: 10.1186/1471-2164-9-626] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Accepted: 12/23/2008] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Mus spretus diverged from Mus musculus over one million years ago. These mice are genetically and phenotypically divergent. Despite the value of utilizing M. musculus and M. spretus for quantitative trait locus (QTL) mapping, relatively little genomic information on M. spretus exists, and most of the available sequence and polymorphic data is for one strain of M. spretus, Spret/Ei. In previous work, we mapped fifteen loci for skin cancer susceptibility using four different M. spretus by M. musculus F1 backcrosses. One locus, skin tumor susceptibility 5 (Skts5) on chromosome 12, shows strong linkage in one cross. RESULTS To identify potential candidate genes for Skts5, we sequenced 65 named and unnamed genes and coding elements mapping to the peak linkage area in outbred spretus, Spret/EiJ, FVB/NJ, and NIH/Ola. We identified polymorphisms in 62 of 65 genes including 122 amino acid substitutions. To look for polymorphisms consistent with the linkage data, we sequenced exons with amino acid polymorphisms in two additional M. spretus strains and one additional M. musculus strain generating 40.1 kb of sequence data. Eight candidate variants were identified that fit with the linkage data. To determine the degree of variation across M. spretus, we conducted phylogenetic analyses. The relatedness of the M. spretus strains at this locus is consistent with the proximity of region of ascertainment of the ancestral mice. CONCLUSION Our analyses suggest that, if Skts5 on chromosome 12 is representative of other regions in the genome, then published genomic data for Spret/EiJ are likely to be of high utility for genomic studies in other M. spretus strains.
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Affiliation(s)
- Kimberly L Mahler
- Division of Human Cancer Genetics, Department of Molecular Virology, Immunology and Medical Genetics, OSU Comprehensive Cancer Center, The Ohio State University, OH, USA.
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Fox AK, Tuch BB, Chuang JH. Measuring the prevalence of regional mutation rates: an analysis of silent substitutions in mammals, fungi, and insects. BMC Evol Biol 2008; 8:186. [PMID: 18588686 PMCID: PMC2447844 DOI: 10.1186/1471-2148-8-186] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Accepted: 06/27/2008] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The patterns of mutation vary both within and across genomes. It has been shown for a few mammals that mutation rates vary within the genome, while for unknown reasons, the sensu stricto yeasts have uniform rates instead. The generality of these observations has been unknown. Here we examine silent site substitutions in a more expansive set (20 mammals, 27 fungi, 4 insects) to determine why some genomes demonstrate this mosaic distribution and why others are uniform. RESULTS We applied several intragene and intergene correlation tests to measure regional substitution patterns. Assuming that silent sites are a reasonable approximation to neutrally mutating sequence, our results show that all multicellular eukaryotes exhibit mutational heterogeneity. In striking contrast, all fungi are mutationally uniform - with the exception of three Candida species: C. albicans, C. dubliniensis, and C. tropicalis. We speculate that aspects of replication timing may be responsible for distinguishing these species. Our analysis also reveals classes of genes whose silent sites behave anomalously with respect to the mutational background in many species, indicating prevalent selective pressures. Genes associated with nucleotide binding or gene regulation have consistently low silent substitution rates in every mammalian species, as well as multiple fungi. On the other hand, receptor genes repeatedly exhibit high silent substitution rates, suggesting they have been influenced by diversifying selection. CONCLUSION Our findings provide a framework for understanding the regional mutational properties of eukaryotes, revealing a sharp difference between fungi and multicellular species. They also elucidate common selective pressures acting on eukaryotic silent sites, with frequent evidence for both purifying and diversifying selection.
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Affiliation(s)
- Aleah K Fox
- Department of Biology, Boston College, Chestnut Hill, MA 02467, USA.
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Brinkmeyer-Langford C, Raudsepp T, Gustafson-Seabury A, Chowdhary BP. A BAC contig map over the proximal approximately 3.3 Mb region of horse chromosome 21. Cytogenet Genome Res 2008; 120:164-72. [PMID: 18467843 DOI: 10.1159/000118758] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2007] [Indexed: 11/19/2022] Open
Abstract
A total of 207 BAC clones containing 155 loci were isolated and arranged into a map of linearly ordered overlapping clones over the proximal part of horse chromosome 21 (ECA21), which corresponds to the proximal half of the short arm of human chromosome 19 (HSA19p) and part of HSA5. The clones form two contigs - each corresponding to the respective human chromosomes - that are estimated to be separated by a gap of approximately 200 kb. Of the 155 markers present in the two contigs, 141 (33 genes and 108 STS) were generated and mapped in this study. The BACs provide a 4-5x coverage of the region and span an estimated length of approximately 3.3 Mb. The region presently contains one mapped marker per 22 kb on average, which represents a major improvement over the previous resolution of one marker per 380 kb obtained through the generation of a dense RH map for this segment. Dual color fluorescence in situ hybridization on metaphase and interphase chromosomes verified the relative order of some of the BACs and helped to orient them accurately in the contigs. Despite having similar gene order and content, the equine region covered by the contigs appears to be distinctly smaller than the corresponding region in human (3.3 Mb vs. 5.5-6 Mb) because the latter harbors a host of repetitive elements and gene families unique to humans/primates. Considering limited representation of the region in the latest version of the horse whole genome sequence EquCab2, the dense map developed in this study will prove useful for the assembly and annotation of the sequence data on ECA21 and will be instrumental in rapid search and isolation of candidate genes for traits mapped to this region.
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Affiliation(s)
- C Brinkmeyer-Langford
- Department of Veterinary Integrative Biomedical Sciences, College of Veterinary Medicine, Texas A&M University, College Station, TX, USA
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29
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Kemkemer C, Kohn M, Kehrer-Sawatzki H, Minich P, Högel J, Froenicke L, Hameister H. Reconstruction of the ancestral ferungulate karyotype by electronic chromosome painting (E-painting). Chromosome Res 2007; 14:899-907. [PMID: 17195924 DOI: 10.1007/s10577-006-1097-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2006] [Revised: 10/28/2006] [Accepted: 10/28/2006] [Indexed: 12/14/2022]
Abstract
By comparing high-coverage and high-quality whole genome sequence assemblies it is now possible to reconstruct putative ancestral progenitor karyotypes, here called protokaryotypes. For this study we used the recently described electronic chromosome painting technique (E-painting) to reconstruct the karyotype of the 85 million-year-old (MYA) ferungulate ancestor. This model is primarily based on dog (Canis familiaris) and cattle (Bos taurus) genome data and is highly consistent with comparative gene mapping and chromosome painting data. The protokaryotype bears 23 autosomal chromosome pairs and the sex chromosomes and preserves most of the chromosomal associations described previously for the boreo-eutherian protokaryotype. The model indicates that five interchromosomal rearrangements occurred during the transition from the boreo-eutherian to the ferungulate ancestor. From there on 66 further interchromosomal rearrangements took place in the lineage leading to cattle and 61 further interchromosomal rearrangements in the lineage to dog.
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Affiliation(s)
- Claus Kemkemer
- Institute of Human Genetics, University Ulm, Albert-Einstein-Allee 11, 89070 Ulm, Germany
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